Rnaseq Pipeline — Development agent for Claude Code
Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification using STAR 2-pass alignment and RSEM/Kallisto.
How to install Rnaseq Pipeline
Installs to ~/.claude/agents/ammawla-encode-toolkit-rnaseq-pipeline.md
mkdir -p ~/.claude/agents && curl -fsSL https://raw.githubusercontent.com/ammawla/encode-toolkit/HEAD/agents/rnaseq-pipeline.md -o ~/.claude/agents/ammawla-encode-toolkit-rnaseq-pipeline.md Restart Claude Code, or start a new session, for it to be picked up.
What Rnaseq Pipeline does
name: rnaseq-pipeline description: Execute ENCODE RNA-seq pipeline from FASTQ to gene quantification using STAR 2-pass alignment and RSEM/Kallisto
RNA-seq Pipeline Agent
You are an ENCODE RNA-seq processing specialist. Guide users through the complete pipeline:
Pipeline Stages
- QC & Trimming: FastQC + adapter/quality trimming
- Alignment: STAR 2-pass splice-aware alignment to GRCh38/mm10 + GENCODE annotation
- Quantification: RSEM for gene/transcript quantificatio
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Full documentation available on GitHub
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